Paper or report template

Author 11,2,* , Author 21,2, Author 33, Author 4E4
1Heidelberg University, Centre for Organismal Studies (COS), 69120 Heidelberg, Germany
2Affiliation 2
3Affiliation 3
4Affiliation 4
*Correspondence: xy@cos.uni-heidelberg.de

Abstract

This is a Quarto document. Quarto uses a simple Markdown formatting syntax for authoring HTML, PDF, and MS Word or .odt documents. For more details on using Quarto see https://quarto.org/.

Here is our abstract. We discovered that medaka fish can eat Arabidpopsis shoop apical meristeme cells to regulate energy metabolism (data not shown). Here is some text in bold italic underline and superscript.

Introduction

Sub-intro

Sub-sub-intr

sub-sub-sub-intro
sub-sub-sub-sub-intro

Platynereis dumerilii is a marine annelid… (Ozpolat et al., 2021). It is also the coolest model organism. It lives in shallow sea on seagrass. Ischia is a good sampling location.

it is just like ms word, let’s add a reference (Lyndby et al., 2023; Pavlov, 2006) another one (Marino, 2004; Pavlov, 2006) (Ozpolat et al., 2021; Saile et al., 2023)

Results

Histology of the crocodile (Myburgh et al., 2023)

Adding references

You can add references either by referring to their id in the .bib file e.g., (Marinković et al., 2019), or by switching to the visual editor (Cogwheel in the .Rmd menu -> Use Visual Editor). (Jacobs and Ryu, 2023; Jokura et al., 2023)

In the visual editor mode, go to ‘Insert’ -> @ Citation You can select a Zotero library, PubMed, CrossRef etc. and insert the citations. (Jacobs and Ryu, 2023)

Nile croc paper (Pooley and Gans, 1976)

One easy and techy way is to use the command line:

curl -LH "Accept: application/x-bibtex" https://doi.org/10.7554/eLife.91258.1 >> references.bib

#make sure to use >> and not > otherwise you will overwrite your file!

The references are stored in manuscript/references.bib (needs to be defined in the Yaml header). This file will automatically updated when you insert a new reference through the Visual editor > Insert > Citations.

(Lohmann et al., 2001; Lohmann et al., 2023; Ozpolat et al., 2021; Saile et al., 2023; Wu et al., 2020)

In this documents, references will be formatted in the style of eLife. This is defined in the Yaml header under: csl: elife.csl. The elife.csl file is saved in the /manuscript folder.

If you would like to use a different citation format, download the respective .csl file (e.g., from the Zotero style repository https://www.zotero.org/styles), save it in the /manuscript folder of the project and change the Yaml to csl: your_favourite_journal.csl.

Now edit the text, add a few references and press -> Render and see how the changes show up on the rendered document. It is easier and faster to render your document to html. You will get a very nice dynamic layout that you can read in the browser (use Firefox). You can also render into pdf, but you need to install a version of latex for that. An easy alternative to generate a nice pdf is to open the html version in a browser (in this case Chrome gives the best results) and print to a pdf file.

Inserting figures

You can add your figures into the rendered document. We saved the figures into /manuscript/figures or /manuscript/figure_supplements and can insert them from there. We use knitr::include_graphics for this. The title and legend can also be edited, as well as the width of the output figure.

Figure 1. A figure (A) A nice picture. (B) legend. (C)
(D)

Figure 1. Our nice figure from yesterday (A) A nice picture. (B) legend. (C)
(D)

Adding equations

Equations can also be inserted, Insert -> Display Math:

\[ \bar{X} = \frac{\sum_{i=1}^{n} x_{i}}{n} \]


Sourcing code and working with variable

The mean value of Nanog expression was 0.0909 indicating that Nanog is downregulated. The ‘analysis/scripts/statistics_for_paper.R’ script is sourced and it runs but the output is not included in the knitted output. But we can access the variables defined in the sourced script simply by adding ` r var_name ` between ` backticks, in this case max_PRC value is 21 (now this number comes from our sourced script).

If we update the data, the script can recalculate the variable we want to refer to in the text and update the number.

Inserting comments

Inserting comments: You can also use the visual editor and insert -> comment.

Test comment here.

Acknowledgements

We would like to thank the Jekely lab for the R project template we used to write this paper. This work was funded by xy funding agency.

Materials and Methods

You can insert tables from source data, such as .csv or Excel files and render them in html with the tinytable package.

Alternatively, you can use the Markdown grid table format. For more complex tables, you can use the tablesgenerator online grid table editor/converter (e.g. converts csv or excel files).

The output may differ between html and pdf, for most consistent results use the grid table format described here.

Key Resources Table

Warning: The `placement` argument in `tt()` is deprecated. Please use this
instead: `theme_tt(table, 'placement')`
Reagent type (species) or resource Designation Source or reference Identifiers Additional information
biological sample (N. vectensis) larval, juvenile and adult N. vectensis Specimens obtained form the Marine Invertebrate Culture Unit of the University of Exeter N/A NA
biological sample (cDNA) cDNA obtained from N. vectensis this study N/A RNA extracted with Trizol and cDNA synthesized with cDNA synthesis kit according to manufacturers recommendation
biological sample (peptide extract) peptide extracts obtained from N. vectensis this study N/A Peptides extracted from N. vectensis according to protocol explained in Material and Methods
genetic reagent (cDNA synthesis) SuperScript™ III First-Strand Synthesis System Invitrogen (from ThermoFisher) 18080051 NA
genetic reagent (Polymerase) Q5® Hot Start High-Fidelity DNA Polymerase  New England Biolabs M0493L NA
genetic reagent (DNA assembly) NEBuilder® HiFi DNA Assembly Master Mix New England Biolabs E2621L NA
genetic reagent (restriction enzyme) EcoRV restriction enzyme New England Biolabs R3195L NA
genetic reagent (restriction enzyme) Afl2 restriction enzyme New England Biolabs R0520L NA
Grid Table example
Col1 Col2 Col3 Col4 Col5
a b c d e
d
v n f f

Complex grid table example

This table was generated by tt() as the output of an r chunk in a Quarto doc. For larger multi-page tables, this method gives correct page breaks in the pdf and html outputs. You can change the relative column widths with {tbl-colwidths=“[10,20,20,20,30]”} placed after the table caption declaration at the end.

More complex Grid Table example
Reagent type (species) or resource Designation Source or reference Identifiers Additional information
biological sample (N. vectensis) larval, juvenile and adult N. vectensis Specimens obtained form the Marine Invertebrate Culture Unit of the University of Exeter N/A NA
biological sample (cDNA) cDNA obtained from N. vectensis this study N/A RNA extracted with Trizol and cDNA synthesized with cDNA synthesis kit according to manufacturers recommendation
biological sample (peptide extract) peptide extracts obtained from N. vectensis this study N/A Peptides extracted from N. vectensis according to protocol explained in Material and Methods
genetic reagent (cDNA synthesis) SuperScript™ III First-Strand Synthesis System Invitrogen (from ThermoFisher) 18080051 NA
genetic reagent (Polymerase) Q5® Hot Start High-Fidelity DNA Polymerase New England Biolabs M0493L NA
genetic reagent (DNA assembly) NEBuilder® HiFi DNA Assembly Master Mix New England Biolabs E2621L NA
genetic reagent (restriction enzyme) EcoRV restriction enzyme New England Biolabs R3195L NA
genetic reagent (restriction enzyme) Afl2 restriction enzyme New England Biolabs R0520L NA

A table from tablesgenerator

gene days raw_data ct_value dt_ct x2_dct mean2dct sd2dct
Nanog d0 J1 22,491 6,956000000000000 0,008054439990584290 0,080889155034072582 9,40847959654144e-02
Nanog d0 J2 19,877 4,395999999999999 0,047497651762547402 0,080889155034072582 9,40847959654144e-02
Nanog d0 J3 19,164 2,418000000000003 0,187115373349086067 0,080889155034072582 9,40847959654144e-02
Nanog d7 J4 21,177 4,667999999999999 0,039336161672026825 0,031927117712361432 7,83151167074938e-03
Nanog d7 J5 21,812 4,934000000000001 0,032712821311705470 0,031927117712361432 7,83151167074938e-03
Nanog d7 J6 22,303 5,397000000000002 0,023732370153351993 0,031927117712361432 7,83151167074938e-03
Nanog d11 J7 22,930 7,436000000000000 0,005774853247163445 0,145298820021575043 2,41582234272199e-01
Nanog d11 J8 22,915 7,412999999999998 0,005867655964613011 0,145298820021575043 2,41582234272199e-01
Nanog d11 J9 17,831 1,236999999999998 0,424253950852948647 0,145298820021575043 2,41582234272199e-01
Nanog d15 J10 15,848 1,252000000000001 0,419865746472069978 0,159625405875477383 2,25708832493508e-01
Nanog d15 J11 20,295 4,581000000000001 0,041781265481410403 0,159625405875477383 2,25708832493508e-01
Nanog d15 J12 20,492 5,859000000000002 0,017229205672951744 0,159625405875477383 2,25708832493508e-01
Nanog d16 J13 21,168 5,347999999999999 0,024552266145861899 0,036597442578737135 1,04525811603947e-02
Nanog d16 J14 20,984 4,575000000000003 0,041955390711883152 0,036597442578737135 1,04525811603947e-02
Nanog d16 J15 20,974 4,530000000000001 0,043284670878466366 0,036597442578737135 1,04525811603947e-02
oct4 d0 K1 17,910 2,375000000000000 0,192776353175992593 0,311031348034201960 1,83714182145261e-01
oct4 d0 K2 17,681 2,200000000000001 0,217637640824030865 0,311031348034201960 1,83714182145261e-01
oct4 d0 K3 17,682 0,936000000000000 0,522680050102582450 0,311031348034201960 1,83714182145261e-01
oct4 d7 K4 21,113 4,603999999999999 0,041120453907156532 0,049755310269836310 1,48819426940308e-02
oct4 d7 K5 21,479 4,600999999999999 0,041206050452886472 0,049755310269836310 1,48819426940308e-02
oct4 d7 K6 20,807 3,901000000000000 0,066939426449465933 0,049755310269836310 1,48819426940308e-02
oct4 d11 K7 19,617 4,123000000000001 0,057392260143807688 0,090862010483616931 4,52910618365094e-02
oct4 d11 K8 19,282 3,779999999999999 0,072795849154278516 0,090862010483616931 4,52910618365094e-02
oct4 d11 K9 19,406 2,811999999999998 0,142397922152764589 0,090862010483616931 4,52910618365094e-02
oct4 d15 K10 18,640 4,044000000000000 0,060622619396358407 0,089412757950352861 4,08917973218200e-02
oct4 d15 K11 18,590 2,875999999999999 0,136219014026666085 0,089412757950352861 4,08917973218200e-02
oct4 d15 K12 18,441 3,808000000000000 0,071396640428034092 0,089412757950352861 4,08917973218200e-02
oct4 d16 K13 19,843 4,023000000000000 0,061511501377112525 0,121511212049720957 5,39049236892096e-02
oct4 d16 K14 19,001 2,592000000000002 0,165855642574644940 0,121511212049720957 5,39049236892096e-02
oct4 d16 K15 19,310 2,866000000000000 0,137166492197405399 0,121511212049720957 5,39049236892096e-02
sox2 d0 L1 22,212 6,677000000000000 0,009772883438384896 0,012106883312601676 5,00188213381361e-03
sox2 d0 L2 22,326 6,845000000000001 0,008698606392411608 0,012106883312601676 5,00188213381361e-03
sox2 d0 L3 22,554 5,808000000000000 0,017849160107008523 0,012106883312601676 5,00188213381361e-03
sox2 d7 L4 23,729 7,219999999999999 0,006707542472169956 0,008115146531345131 1,23319175000228e-03
sox2 d7 L5 23,673 6,794999999999998 0,009005362084366138 0,008115146531345131 1,23319175000228e-03
sox2 d7 L6 23,762 6,856000000000002 0,008632535037499301 0,008115146531345131 1,23319175000228e-03
sox2 d11 L7 23,290 7,795999999999999 0,004499561102927181 0,005068258267873239 1,39821485937085e-03
sox2 d11 L8 23,452 7,950000000000001 0,004044003608755378 0,005068258267873239 1,39821485937085e-03
sox2 d11 L9 23,824 7,230000000000000 0,006661210091937160 0,005068258267873239 1,39821485937085e-03
sox2 d15 L10 18,978 4,382000000000001 0,047960815500027662 0,019052009679567623 2,50790414471593e-02
sox2 d15 L11 23,078 7,363999999999999 0,006070369287375391 0,019052009679567623 2,50790414471593e-02
sox2 d15 L12 22,955 8,321999999999999 0,003124844251299816 0,019052009679567623 2,50790414471593e-02
sox2 d16 L13 18,256 2,436000000000000 0,184795303909230241 0,065112130982845073 1,03648699316095e-01
sox2 d16 L14 23,955 7,545999999999999 0,005350910077990494 0,065112130982845073 1,03648699316095e-01
sox2 d16 L15 24,034 7,590000000000000 0,005190178961314499 0,065112130982845073 1,03648699316095e-01
Nestin d0 M1 25,678 10,143000000000001 0,000884408186540842 0,001005919450970835 3,78037724925826e-04
Nestin d0 M2 25,954 10,473000000000001 0,000703578978924766 0,001005919450970835 3,78037724925826e-04
Nestin d0 M3 26,196 9,450000000000003 0,001429771187446897 0,001005919450970835 3,78037724925826e-04
Nestin d7 M4 26,637 10,128000000000000 0,000893651531374930 0,001047338646785763 1,49154536320385e-04
Nestin d7 M5 26,591 9,713000000000001 0,001191504404562717 0,001047338646785763 1,49154536320385e-04
Nestin d7 M6 26,792 9,886000000000003 0,001056860004419641 0,001047338646785763 1,49154536320385e-04
Nestin d11 M7 25,344 9,850000000000001 0,001083563937566254 NA NA
Nestin d11 M8 25,548 10,045999999999998 0,000945916200416630 NA NA
Nestin d11 M9 NA NA NA NA NA
Nestin d15 M10 25,146 10,550000000000001 0,000667011844118357 0,040212093347121759 6,78034116386107e-02
Nestin d15 M11 25,128 9,414000000000000 0,001465897556166378 0,040212093347121759 6,78034116386107e-02
Nestin d15 M12 17,710 3,077000000000002 0,118503370641080533 0,040212093347121759 6,78034116386107e-02
Nestin d16 M13 26,670 10,850000000000001 0,000541781968783127 0,000811307199498398 2,34037441161003e-04
Nestin d16 M14 26,481 10,072000000000003 0,000929021754230271 0,000811307199498398 2,34037441161003e-04
Nestin d16 M15 26,464 10,020000000000000 0,000963117875481796 0,000811307199498398 2,34037441161003e-04
pax6 d0 N1 28,141 12,605999999999998 0,000160404251361007 0,000202563640616283 9,07049173589390e-05
pax6 d0 N2 28,277 12,796000000000001 0,000140611284466474 0,000202563640616283 9,07049173589390e-05
pax6 d0 N3 28,417 11,671000000000003 0,000306675386021368 0,000202563640616283 9,07049173589390e-05
pax6 d7 N4 26,551 10,041999999999998 0,000948542476114878 0,001113850118374157 2,12530157522733e-04
pax6 d7 N5 26,407 9,529000000000000 0,001353583872705483 0,001113850118374157 2,12530157522733e-04
pax6 d7 N6 26,816 9,910000000000000 0,001039424006302109 0,001113850118374157 2,12530157522733e-04
pax6 d11 N7 26,240 10,745999999999999 0,000582279722817692 0,000832785029034435 3,78505530767820e-04
pax6 d11 N8 26,094 10,592000000000001 0,000647873603807208 0,000832785029034435 3,78505530767820e-04
pax6 d11 N9 26,217 9,622999999999998 0,001268201760478404 0,000832785029034435 3,78505530767820e-04
pax6 d15 N10 24,989 10,393000000000001 0,000743695673683233 0,000925553902054457 4,08653936584204e-04
pax6 d15 N11 25,201 9,487000000000000 0,001393568853240116 0,000925553902054457 4,08653936584204e-04
pax6 d15 N12 25,244 10,611000000000001 0,000639397179240022 0,000925553902054457 4,08653936584204e-04
pax6 d16 N13 25,234 9,414000000000001 0,001465897556166376 0,118332806864036216 2,01592584300493e-01
pax6 d16 N14 25,099 8,690000000000001 0,002421304101443331 0,118332806864036216 2,01592584300493e-01
pax6 d16 N15 17,954 1,510000000000002 0,351111218934498925 0,118332806864036216 2,01592584300493e-01
Foxg1 d0 O1 27,995 12,460000000000001 0,000177486879555702 0,000282945149618699 1,74962623637300e-04
Foxg1 d0 O2 27,870 12,389000000000001 0,000186440124262781 0,000282945149618699 1,74962623637300e-04
Foxg1 d0 O3 27,756 11,010000000000002 0,000484908445037615 0,000282945149618699 1,74962623637300e-04
Foxg1 d7 O4 27,679 11,169999999999998 0,000434005215413365 0,000523746522152919 8,78322810890892e-05
Foxg1 d7 O5 27,766 10,887999999999998 0,000527697950214528 0,000523746522152919 8,78322810890892e-05
Foxg1 d7 O6 27,586 10,680000000000000 0,000609536400830865 0,000523746522152919 8,78322810890892e-05
Foxg1 d11 O7 27,338 11,844000000000001 0,000272019934282063 0,288184521683127526 4,98617302108864e-01
Foxg1 d11 O8 27,010 11,508000000000001 0,000343357714822539 0,288184521683127526 4,98617302108864e-01
Foxg1 d11 O9 16,805 0,210999999999999 0,863938187400278057 0,288184521683127526 4,98617302108864e-01
Foxg1 d15 O10 26,363 11,766999999999999 0,000286932697368108 0,000345700735619899 1,54341824432769e-04
Foxg1 d15 O11 26,621 10,906999999999998 0,000520793838296761 0,000345700735619899 1,54341824432769e-04
Foxg1 d15 O12 26,723 12,090000000000000 0,000229375671194827 0,000345700735619899 1,54341824432769e-04
Foxg1 d16 O13 26,943 11,123000000000001 0,000448377032373498 0,000619126191915002 1,48774900949806e-04
Foxg1 d16 O14 26,847 10,438000000000002 0,000720856643399820 0,000619126191915002 1,48774900949806e-04
Foxg1 d16 O15 26,949 10,505000000000003 0,000688144899971688 0,000619126191915002 1,48774900949806e-04
GAPDH d0 P1 15,535 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d0 P2 15,481 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d0 P3 16,746 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d7 P4 16,509 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d7 P5 16,878 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d7 P6 16,906 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d11 P7 15,494 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d11 P8 15,502 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d11 P9 16,594 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d15 P10 14,596 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d15 P11 15,714 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d15 P12 14,633 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d16 P13 15,820 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d16 P14 16,409 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00
GAPDH d16 P15 16,444 0,000000000000000 1,000000000000000000 1,000000000000000000 0,00000000000000e+00

References

References

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Lohmann, J. U., Hong, R. L., Hobe, M., Busch, M. A., Parcy, F., Simon, R. and Weigel, D. (2001). A Molecular Link between Stem Cell Regulation and Floral Patterning in Arabidopsis. Cell 105, 793–803.
Lohmann, J., de Luxán-Hernández, C., Gao, Y., Zoschke, R. and Weingartner, M. (2023). Arabidopsis translation factor eEF1Bγ impacts plant development and is associated with heat-induced cytoplasmic foci. Journal of Experimental Botany 74, 2585–2602.
Lyndby, N. H., Murthy, S., Bessette, S., Jakobsen, S. L., Meibom, A. and Kühl, M. (2023). Non-invasive investigation of the morphology and optical properties of the upside-down jellyfishCassiopeawith optical coherence tomography.
Marinković, M., Berger, J. and Jékely, G. (2019). Neuronal coordination of motile cilia in locomotion and feeding. Philosophical Transactions of the Royal Society B: Biological Sciences 375, 20190165.
Marino, L. (2004). Dolphin cognition. Current Biology 14, R910–R911.
Myburgh, A., Myburgh, J., Steyl, J., Downs, C. T., Botha, H., Robinson, L. and Woodborne, S. (2023). The histology and growth rate of Nile crocodile (Crocodylus niloticus) claws. Journal of Morphology 284,.
Ozpolat, B. D., Randel, N., Williams, E. A., Bezares-Calderón, L. A., Andreatta, G., Balavoine, G., Bertucci, P. Y., Ferrier, D. E. K., Gambi, M. C., Gazave, E., et al. (2021). The Nereid on the rise: Platynereis as a model system. Zenodo.
Pavlov, V. V. (2006). Dolphin skin as a natural anisotropic compliant wall. Bioinspiration & Biomimetics 1, 31–40.
Pooley, A. C. and Gans, C. (1976). The nile crocodile. Scientific American 234, 114–125.
Saile, J., Wießner-Kroh, T., Erbstein, K., Obermüller, D. M., Pfeiffer, A., Janocha, D., Lohmann, J. and Wachter, A. (2023). SNF1-RELATED KINASE 1 and TARGET OF RAPAMYCIN control light-responsive splicing events and developmental characteristics in etiolated Arabidopsis seedlings. The Plant Cell 35, 3413–3428.
Wu, H., Qu, X., Dong, Z., Luo, L., Shao, C., Forner, J., Lohmann, J. U., Su, M., Xu, M., Liu, X., et al. (2020). WUSCHEL triggers innate antiviral immunity in plant stem cells. Science 370, 227–231.